We obtained genotype data for the Women’s Health Initiative (WHI)19 (link) study from dbGaP (http://www.ncbi.nlm.nih.gov/gap ). The dataset included 8,421 African Americans genotyped on Affymetrix 6.0. We removed SNPs with genotype call rates < 90%, HWE P < 10−6, or MAF < 1%, resulting in 829,370 SNPs passing quality control criteria. For our imputation experiments we masked every 10th SNP and repeated in sliding windows, such that each analysis was informed by ~90% of the array SNPs and every array SNP was imputed exactly once.
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Imputation of African American Genotypes
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Corresponding Organization : University of Oxford
Other organizations : University of Chicago, University of Michigan–Ann Arbor
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Protocol cited in 294 other protocols
Variable analysis
independent variables
- None explicitly mentioned
- None explicitly mentioned
- SNPs with genotype call rates < 90%
- SNPs with HWE P < 10^-6
- SNPs with MAF < 1%
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